So with miracle day representing a massive change in the look feel and format of the show, should we get a throw away scene in 6 or 7 where the doctor see's something that reminds him of jack and mumbles something along the lines of how big would jacks ego be if he new a universe was created around him as a result of the pandorica?

this would then let torchwood establish its roots which seem to be getting stronger as a stand alone show free from the shadow of its parent show

I've thought about this myself, and there is a similar thread about whether or not it's still part of the Whoniverse, and to me I think TW has always done really well to establish itself in its own right. There has always, and no doubt will always be ties to the main show, but I don't think TW is in DW's shadow by a long shot. COE for example was as far from DW as you can get and while you still knew it was part of the larger Whoniverse, it only mentioned the link one time

Maybe shadow was the wrong word, but you have backed my point COE is so un DW compared to series 1 and 2 thats what made me think it, i mean ok there is the bit with jack in the end of time which was obviously set after COE so they were acknowledging each other, but SJA has already had the 11th doctor in the show linking the two shows. yes tenuously you could say that the vortex manipulator in the pandorica opens could be from jack being a tenuous link, but it is going in a direction away from doctor who which isn't a bad thing at all but is it doctor who enough still to be part of the whoniverse?I would love to see capt john or billis manger to return but alas with the new direction of the show i don't think we ever will

I think it is ok as it is at the moment. There will always be links because of the crossovers, so nobody could argue that it isn't the same 'Whoniverse' but the links are distant enough that TW can stand on it's own two feet. For now I think they have a good balance, but you don't know how much that might change in the future I guess.

One thing I think TW has always managed to do is stand on it's own two feet. It may never have fully escaped the shadow of Doctor Who, but realistically, why would it want to, anyway? I don't think it needs it's own universe. I think it fits nicely into the one it's in.